I want to separate the software and physical part of an access point into two different equipments.
As a first step, I have installed hostapd in an Ubuntu server machine. How can we link hostapd to a physical wireless card located in another machine via ethernet?
P.S.: I have an Atheros chipset, AR9271, that supports monitor mode and works well as an AP with normal configuration of hostapd.
You can't.
Hostapd needs low-level access to the wireless NIC, it's not something you can do over the network from a different machine (I don't see the point, and latency won't allow it anyway).
What you can do though is tell Hostapd to use a bridge (it has a specific configuration directive for this) that includes the Ethernet card of the server; that way you can put your DHCP and/or DNS server on another machine and connect the AP to it.
You can also configure Hostapd to authenticate using a remote Radius server so that user management is done on a different machine.